Scientific

MK5 Microarray Data

Affected Genes - Ontology Breakdown - Gene Enrichment - Proteome Analysis

These are the micro-array results of a differential gene expression microarray experiments and the subsequent analysis steps performed on them. The up/down- regulation ratio was obtained by measuring WT cells against MK5 activated cells. See material and methods for technical information as well as the data usage policy.

Proteome Analysis

Below the proteome analysis is presented. The analysis methods are presented in the paper Propagating Differential Gene Expression in Protein Interaction Networks. If you are interested in the most reliable results choose the

  • value_type as 'ranked' since this provides a very robust analysis method.
  • intercation map as 'high confidence'
  • network_comparison type as 'Divided' since this leads to a natural grouping of similar proteins
  • filtered as 'true' since this will only use the microarray measurements that have a sufficiently large confidence level.

    • Navigation/Query Panel:
    Click on the attribute name to hide/unhide it. The green arrows can be used to shift columns left/right. Exact word match is written as =..., regular expressions can be matched with ~.... To select all values larger or equal than use >.... This would be <... for values smaller or equal than. To select all values within a specific range use [...,...].
    Rank Gene description Hugo Value Type Network Comparison Type Interaction Map red Filtered green network_comparison
    Results: HTML CSV LaTeX Showing element 1341 to 1390 of 33156 in total
    Network Comparison Type  : Divided
    Filtered  : 1
    Rank
    		description
    		Hugo
    		Value Type
    		Interaction Map
    		red
    		green
    		network_comparison
    168 proto-oncogene tyrosine-protein kinase fer (ec 2.7.1.112) (p94-fer) (c-fer). [swissprot;acc:p16591] FER Ranked Low confidence 216.796 205.073 1.05717
    retinal short-chain dehydrogenase/reductase 3. [refseq;acc:nm_016246] HSD17B14 Squared High confidence 173408 242989 1.40126
    ring finger protein 20. [refseq;acc:nm_019592] RNF20 Low confidence 53551.4 48045.1 1.11461
    small nuclear ribonucleoprotein sm d3 (snrnp core protein d3) (sm-d3). [swissprot;acc:p43331] SNRPD3 Rooted High confidence 56.3709 65.8949 1.16895
    169 60s ribosomal protein l29 (cell surface heparin binding protein hip). [swissprot;acc:p47914] RPL29 Ranked Low confidence 216.79 205.07 1.05715
    apg3p; pc3-96 protein. [refseq;acc:nm_022488] ATG3 High confidence 82.5916 98.0548 1.18722
    beta-arrestin 1 (arrestin, beta 1). [swissprot;acc:p49407] ARRB1 Rooted Low confidence 72.4389 77.1711 1.06533
    cop9 constitutive photomorphogenic homolog subunit 3; cop9 complex subunit 3; jab1-containing signalosome subunit 3. [refseq;acc:nm_003653] COPS3 High confidence 62.762 53.7761 1.1671
    cytohesin 3 (arf nucleotide-binding site opener 3) (arno3 protein) (general receptor of phosphoinositides 1) (grp1). [swissprot;acc:o43739] PSCD3 Measured Low confidence 12375.5 11435.8 1.08217
    melanoma-associated antigen 10 (mage-10 antigen). [swissprot;acc:p43363] MAGEA10 High confidence 23693.7 18263 1.29736
    rna-binding protein 10 (rna binding motif protein 10) (dxs8237e). [swissprot;acc:p98175] RBM10 Squared Low confidence 67930.9 60946.6 1.1146
    symplekin. [swissprot;acc:q92797] SYMPK High confidence 124118 88668.8 1.39979
    170 amyloid beta a4 precursor protein-binding family a member 1 (neuron- specific x11 protein) (neuronal munc18-1-interacting protein 1) (mint-1) (adapter protein x11alpha). [swissprot;acc:q02410] APBA1 Measured Low confidence 6131.26 6633.65 1.08194
    b9 protein; likely ortholog of mouse endothelial precursor protein b9. [refseq;acc:nm_015681] B9D1 Rooted High confidence 53.4993 45.9227 1.16499
    cytidine triphosphate synthase ii; ctp synthetase type 2; utp-ammonia ligase; ctp synthetase isoform; cytidine 5'-triphosphate synthetase 2. [refseq;acc:nm_019857] CTPS2 Squared 96730.5 69286.7 1.39609
    inad-like protein isoform 3; pdz domain protein (drosophila inad-like); protein associated to tight junctions; pals1-associated tight junction protein; inactivation no after-potential d-like protein. [refseq;acc:nm_005799] INADL Low confidence 67882.7 60913.7 1.11441
    melanoma-associated antigen b1 (mage-b1 antigen) (mage-xp antigen) (dss-ahc critical interval mage superfamily 10) (dam10). [swissprot;acc:p43366] MAGEB4 Measured High confidence 23693.7 18263 1.29736
    nucleolysin tia-1 (rna-binding protein tia-1) (p40-tia-1) [contains: p15-tia-1]. [swissprot;acc:p31483] TIA1 Ranked 227.199 192.715 1.17894
    oligopeptide transporter, small intestine isoform (peptide transporter 1) (intestinal h+/peptide cotransporter) (solute carrier family 15, member 1). [swissprot;acc:p46059] SLC15A1 Rooted Low confidence 70.7428 75.3259 1.06479
    proto-oncogene tyrosine-protein kinase fes/fps (ec 2.7.1.112) (c-fes). [swissprot;acc:p07332] FES Ranked 216.783 205.066 1.05714
    171 ctp synthase (ec 6.3.4.2) (utp--ammonia ligase) (ctp synthetase). [swissprot;acc:p17812] CTPS Squared High confidence 96602.7 69211.2 1.39577
    forkhead box protein p3 (zinc finger protein jm2) (scurfin). [swissprot;acc:q9bzs1] FOXP3 Ranked Low confidence 219.889 208.064 1.05683
    hira-interacting protein 5 (cgi-33). [swissprot;acc:q9ums0] NFU1 Rooted 96.9641 103.242 1.06474
    lag1 longevity assurance homolog 2 isoform 1; l3 pigment; tumor metastasis-suppressor. [refseq;acc:nm_022075] LASS2 High confidence 61.6639 71.7355 1.16333
    melanoma-associated antigen d2 (mage-d2 antigen) (breast cancer associated gene 1 protein) (bcg-1) (11b6) (hepatocellular carcinoma associated protein jcl-1). [swissprot;acc:q9unf1] MAGED2 Measured 23693.7 18263 1.29736
    multiple pdz domain protein. [refseq;acc:nm_003829] MPDZ Squared Low confidence 67876.4 60909.3 1.11438
    nucleolysin tiar (tia-1 related protein). [swissprot;acc:q01085] TIAL1 Ranked High confidence 227.202 192.823 1.17829
    sentrin-specific protease 8 (ec 3.4.22.-) (sentrin/sumo-specific protease senp8) (cysteine protease fksg8). [swissprot;acc:q96ld8] SENP8 Measured Low confidence 7012.61 7584.69 1.08158
    172 cg9578-like; yeast ypr037w and worm c02c2.6 predicted proteins-like. [refseq;acc:nm_152902] TIPRL Ranked High confidence 174.667 205.556 1.17685
    f-actin capping protein alpha-1 subunit (capz alpha-1). [swissprot;acc:p52907] CAPZA1 Low confidence 213.671 202.205 1.0567
    likely ortholog of mouse variant polyadenylation protein cstf-64. [refseq;acc:nm_015235] CSTF2T Squared High confidence 121579 87259.3 1.39331
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A Rooted Low confidence 65.0717 69.26 1.06436
    splicing factor 3b subunit 1 (spliceosome associated protein 155) (sap 155) (sf3b155) (pre-mrna splicing factor sf3b 155 kda subunit). [swissprot;acc:o75533] SF3B1 High confidence 56.7592 65.9889 1.16261
    trophinin. [swissprot;acc:q12816] TRO Measured 23693.7 18263 1.29736
    ubiquitin-like protein nedd8. [swissprot;acc:q15843] NEDD8 Low confidence 7012.61 7584.69 1.08158
    ww domain binding protein 11; npw38-binding protein npwbp; sh3 domain-binding protein snp70. [refseq;acc:nm_016312] WBP11 Squared 67872.2 60906.5 1.11437
    173 28s ribosomal protein s17, mitochondrial precursor (mrp-s17) (hspc011). [swissprot;acc:q9y2r5] MRPS17 Rooted High confidence 145.551 168.796 1.1597
    breast cancer antiestrogen resistance 3. [refseq;acc:nm_003567] BCAR3 Measured 4579.34 5940.64 1.29727
    elac homolog 2; putative prostate cancer susceptibility protein; elac (e. coli) homolog 2. [refseq;acc:nm_018127] ELAC2 Squared Low confidence 67872.2 60906.5 1.11437
    sad1/unc-84 protein-like 1. [swissprot;acc:o94901] UNC84A Ranked 221.678 209.795 1.05664
    septin 2 (nedd5 protein homolog). [swissprot;acc:q15019] SEPT2 Measured 10168.5 10996.7 1.08145
    septin 4 (peanut-like protein 2) (brain protein h5) (cell division control-related protein 2) (hcdcrel-2) (bradeion beta) (ce5b3 beta) (cerebral protein-7) (hucep-7). [swissprot;acc:o43236] SEPT4 Squared High confidence 82624.3 115061 1.39258
    small nuclear ribonucleoprotein sm d1 (snrnp core protein d1) (sm-d1) (sm-d autoantigen). [swissprot;acc:p13641] SNRPD1 Ranked 227.032 193.056 1.17599
    u1 small nuclear ribonucleoprotein a (u1 snrnp a protein). [swissprot;acc:p09012] SNRPA Rooted Low confidence 70.5964 75.1199 1.06408
    174 cytohesin 4. [swissprot;acc:q9uia0] PSCD4 Measured 12315 11390.6 1.08115
    dgcr14 protein (digeorge syndrome critical region 14) (es2 protein). [swissprot;acc:q96df8] DGCR14 Ranked High confidence 335 286 1.17133
    forkhead box protein p1 (hspc215). [swissprot;acc:q9h334] FOXP1 Low confidence 219.6 207.907 1.05624
    mad protein (max dimerizer). [swissprot;acc:q05195] MXD1 Measured High confidence 4455.95 5774.03 1.2958
    pantothenate kinase 1 (ec 2.7.1.33) (pantothenic acid kinase 1) (hpank1) (hpank). [swissprot;acc:q8te04] PANK1 Rooted 145.551 168.796 1.1597
    rna-binding protein 5 (rna binding motif protein 5) (putative tumor suppressor luca15) (g15 protein). [swissprot;acc:p52756] RBM5 Squared Low confidence 67801.5 60858 1.11409

    Legend:
    - Rank is the rank after comparing the two networks
    - Gene is the ensembl human gene identifier measured by 1 or more probes on the microarray
    - Hugo is the HGNC identifier if it exists
    - Value Type describes how the microarray measurement was processed. Ranked indicates that we sorted all measurements and use the rank as red and green value. Measured is the normal measurement. Squared and Rooted are the square and square root respecitcely. This might be valueable to compensate for non linear light distributions.
    - Network Comparison Type describes whether we divided the red and green types or whether we sutractcted them
    - Interaction Map specifies whether we used only the hig hconfidence protein-protein interactions or also included the low confidence interactions.
    - Filtered specifies whether we only included the high confidence microarry measurements or not.
    - http://analysis.yellowcouch.org/